|
| Status |
Public on Nov 29, 2012 |
| Title |
7dpf.b_sib.cy5_mut.cy3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
entpd5_7dpfb_sibling
|
| Organism |
Danio rerio |
| Characteristics |
genotype/variation: wild type
tissue: whole embryos at 7 dpf
|
| Growth protocol |
Embryos were raised in standard E3 medium at 28 degrees Celcius. At 6 dpf mutant were separated from siblings by an in vivo skeletal staining as mutants fail to mineralize their skeleton. At 7 dpf, embryos were sacrificed by an overdosis of ms222 and frozen in liquid nitrogen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from (n=30) entpd5 mutants versus siblings was isolated using the Rnaesy mini kit (Qiagen) according to the manufactures protocol.
|
| Label |
cy5
|
| Label protocol |
cDNA synthesis and labeling were performed using the two color Low Input Quick-Amp labeling kit (5190-2306, Agilent Technologies) and samples were purified using the Rneasy Mini kit (Qiagen). Concentration and cy3 and cy5 incorporation were determined using a nanodrop spectrophotometer.
|
| |
|
| Channel 2 |
| Source name |
entpd5_7dpfb_mutant
|
| Organism |
Danio rerio |
| Characteristics |
genotype/variation: entpd5 mutant
tissue: whole embryos at 7 dpf
phenotype/selection: failure to mineralize their skeleton at 7 dpf
|
| Growth protocol |
Embryos were raised in standard E3 medium at 28 degrees Celcius. At 6 dpf mutant were separated from siblings by an in vivo skeletal staining as mutants fail to mineralize their skeleton. At 7 dpf, embryos were sacrificed by an overdosis of ms222 and frozen in liquid nitrogen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from (n=30) entpd5 mutants versus siblings was isolated using the Rnaesy mini kit (Qiagen) according to the manufactures protocol.
|
| Label |
cy3
|
| Label protocol |
cDNA synthesis and labeling were performed using the two color Low Input Quick-Amp labeling kit (5190-2306, Agilent Technologies) and samples were purified using the Rneasy Mini kit (Qiagen). Concentration and cy3 and cy5 incorporation were determined using a nanodrop spectrophotometer.
|
| |
|
| |
| Hybridization protocol |
Labeled samples were hybridized for 17 hours at 60 degrees Celcius to a 4x44K zebrafish expression array using the Gene Expression Hybrdization Kit (Agilent technologies). Arrays were washed according to the manufactures protocol.
|
| Scan protocol |
The microarray was scanned using the G2505C Agilent DNA microarray scanner using default parameters.
|
| Description |
Samples were run in dye swap
Sample 4
|
| Data processing |
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
Feb 13, 2012 |
| Last update date |
Nov 30, 2012 |
| Contact name |
Leonie Huitema |
| E-mail(s) |
l.huitema@hubrecht.eu
|
| Phone |
+3130 212 1920
|
| Fax |
+3130 251 64 64
|
| URL |
http://www.hubrecht.eu/research/schulte-merker/index.html
|
| Organization name |
Hubrecht Institute
|
| Department |
Schulte-Merker group
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584CT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6457 |
| Series (1) |
| GSE35737 |
Zebrafish ectonucleoside triphosphate/diphosphohydrolase 5 (entpd5) mutants compared to siblings at 7 dpf |
|
